arXiv subjects

Ali Parviz

Publications and source records attributed to Ali Parviz.

At least 19 recordsLinked to original sources

arXiv2026

Nonlinear Laplacians Improve Signed-Directed Graph Learning

While signed-directed graphs have been studied using linear Laplacians in the design of graph neural networks, relatively little research has focused on developing non-linear Laplacian operators for such networks. We introduce a non-linear Laplacian operator specific to signed and directed networks (NLSD). This non-linear operator extends the concepts of the signed Laplacian for signed graphs and the Laplacian for directed graphs. The NLSD calculates node-specific potentials based on features More precisely, if the potential discrepancy is not aligned with the edge direction, we ignore it (and vice versa) leveraging message-passing techniques only across edges where potential discrepancies align with the edge's direction. Utilizing this novel operator, we propose an efficient spectral GNN framework (NLSD-GNN). We conducted comprehensive evaluations focusing on node classification and link prediction, examining scenarios involving signed, directional, or both types of information. Our findings reveal that this spectral GNN framework not only integrates signed and directional data effectively but also achieves superior performance across diverse datasets.

cs.LG↗

arXiv2026

Reassessing Muon for Matrix Factorization

Muon has recently emerged as a strong optimizer for large-scale deep learning, where it reshapes gradient updates through approximate orthogonalization and has been reported to outperform Adam and AdamW in large language model training. Its empirical success has motivated a growing body of theoretical work that interprets Muon as steepest descent under the spectral norm. Yet it remains unclear which of Muon's advantages stem from its update rule itself and which are artifacts of the scale, architecture, and data of modern deep networks. In this work, we isolate the optimizer from these confounding factors by studying Muon on a simple, well-understood, and spectrally structured problem: low-rank matrix factorization. Through a controlled comparison against carefully tuned adaptive baselines, we find that Muon does not consistently outperform AdamW in this setting and that several previously reported advantages are sensitive to hyperparameter choices. Our results provide a more nuanced picture of when spectrum-aware orthogonalization is beneficial and argue for evaluating modern optimizers on controlled problems in addition to end-to-end benchmarks.

cs.LG↗

arXiv2026

Probabilistic Tiny Recursive Model

Tiny Recursive Models (TRM) solve complex reasoning tasks with a fraction of the parameters of modern large language models (LLMs) by iteratively refining a latent state and final answer. While powerful, their deterministic recursion can lead to convergence at suboptimal solutions, without escape mechanism. A common workaround relies on task-specific input perturbations at test time combined with answer aggregation via voting. We introduce Probabilistic TRM (PTRM), a task-agnostic framework for test-time compute scaling that addresses this limitation through stochastic exploration. PTRM injects Gaussian noise at each deep recursion step, enabling parallel trajectories to explore diverse solution basins, and selects among them using the model's existing Q head (used for early stopping in the original TRM). Without requiring retraining or task-specific augmentations, PTRM enables substantial accuracy gains across benchmarks, including Sudoku-Extreme (87.4% to 98.75%) and on various puzzles from Pencil Puzzle Bench (62.6% to 91.2%). On the latter, PTRM achieves nearly double the accuracy of frontier LLMs (91.2% vs. 55.1%) at less than 0.0001x the cost, using only 7M parameters.

cs.AI↗

arXiv2026

Local Inconsistency Resolution: The Interplay between Attention and Control in Probabilistic Models

We present a generic algorithm for learning and approximate inference with an intuitive epistemic interpretation: iteratively focus on a subset of the model and resolve inconsistencies using the parameters under control. This framework, which we call Local Inconsistency Resolution (LIR) is built upon Probabilistic Dependency Graphs (PDGs), which provide a flexible representational foundation capable of capturing inconsistent beliefs. We show how LIR unifies and generalizes a wide variety of important algorithms in the literature, including the Expectation-Maximization (EM) algorithm, belief propagation, adversarial training, GANs, and GFlowNets. In the last case, LIR actually suggests a more natural loss, which we demonstrate improves GFlowNet convergence. Each method can be recovered as a specific instance of LIR by choosing a procedure to direct focus (attention and control). We implement this algorithm for discrete PDGs and study its properties on synthetically generated PDGs, comparing its behavior to the global optimization semantics of the full PDG.

cs.AI↗

arXiv2026

REAM: Merging Improves Pruning of Experts in LLMs

Mixture-of-Experts (MoE) large language models (LLMs) are among the top-performing architectures. The largest models, often with hundreds of billions of parameters, pose significant memory challenges for deployment. Traditional approaches to reduce memory requirements include weight pruning and quantization. Motivated by the Router-weighted Expert Activation Pruning (REAP) that prunes experts, we propose a novel method, Router-weighted Expert Activation Merging (REAM). Instead of removing experts, REAM groups them and merges their weights, better preserving original performance. We evaluate REAM against REAP and other baselines across multiple MoE LLMs on diverse multiple-choice (MC) question answering and generative (GEN) benchmarks. Our results reveal a trade-off between MC and GEN performance that depends on the mix of calibration data. By controlling the mix of general, math and coding data, we examine the Pareto frontier of this trade-off and show that REAM often outperforms the baselines and in many cases is comparable to the original uncompressed models.

cs.AI↗

arXiv2026

M^4olGen: Multi-Agent, Multi-Stage Molecular Generation under Precise Multi-Property Constraints

Generating molecules that satisfy precise numeric constraints over multiple physicochemical properties is critical and challenging. Although large language models (LLMs) are expressive, they struggle with precise multi-objective control and numeric reasoning without external structure and feedback. We introduce \textbf{M olGen}, a fragment-level, retrieval-augmented, two-stage framework for molecule generation under multi-property constraints. Stage I : Prototype generation: a multi-agent reasoner performs retrieval-anchored, fragment-level edits to produce a candidate near the feasible region. Stage II : RL-based fine-grained optimization: a fragment-level optimizer trained with Group Relative Policy Optimization (GRPO) applies one- or multi-hop refinements to explicitly minimize the property errors toward our target while regulating edit complexity and deviation from the prototype. A large, automatically curated dataset with reasoning chains of fragment edits and measured property deltas underpins both stages, enabling deterministic, reproducible supervision and controllable multi-hop reasoning. Unlike prior work, our framework better reasons about molecules by leveraging fragments and supports controllable refinement toward numeric targets. Experiments on generation under two sets of property constraints (QED, LogP, Molecular Weight and HOMO, LUMO) show consistent gains in validity and precise satisfaction of multi-property targets, outperforming strong LLMs and graph-based algorithms.

cs.AI↗

arXiv2026

LLMs Can't Play Hangman: On the Necessity of a Private Working Memory for Language Agents

As LLMs move from text completion toward autonomous agents, they remain constrained by the standard chat interface, which lacks private working memory. This raises a fundamental question: can agents reliably perform interactive tasks that depend on hidden state? We define Private State Interactive Tasks (PSITs), which require agents to generate and maintain hidden information while producing public responses consistent with a fixed hidden state. We show theoretically that any agent restricted to the public conversation history cannot both keep the secret unresolved in the transcript and respond consistently with a fixed hidden state in PSITs, yielding an architectural impossibility theorem. To empirically validate this limitation, we introduce a self-consistency testing protocol that evaluates whether agents can maintain a hidden secret across forked dialogue branches. Standard chat-based LLMs and retrieval-based memory baselines fail this test regardless of scale, demonstrating that semantic retrieval does not enable true state maintenance. To address this, we propose a novel architecture incorporating an explicit private working memory; we demonstrate that this mechanism restores consistency with a fixed hidden state, establishing private state as a necessary component for PSIT-capable language agents. Our code is available at https://github.com/chandar-lab/Hangman

cs.CL↗

arXiv2025

GraphBench: Next-generation graph learning benchmarking

Machine learning on graphs has made substantial progress across domains such as molecular property prediction and chip design. Yet benchmarking practices remain fragmented, often relying on narrow, task-specific datasets and inconsistent evaluation protocols, hindering reproducibility and broader progress. With the recent popularity of graph foundation models, these weaknesses have become apparent, as existing benchmarks are insufficient for thorough evaluation. To address these challenges, we introduce GraphBench, a comprehensive benchmark suite spanning diverse real-world domains and task settings, including node-level, edge-level, graph-level, and generative tasks. GraphBench provides standardized evaluation protocols, including consistent dataset splits and metrics for assessing out-of-distribution generalization across selected tasks, as well as a unified hyperparameter-tuning framework. We further evaluate GraphBench with recent message-passing neural networks and graph transformer models, establishing principled baselines for future research. See www.graphbench.io for further details.

cs.LG↗

arXiv2025

TGM: a Modular and Efficient Library for Machine Learning on Temporal Graphs

Well-designed open-source software drives progress in Machine Learning (ML) research. While static graph ML enjoys mature frameworks like PyTorch Geometric and DGL, ML for temporal graphs (TG), networks that evolve over time, lacks comparable infrastructure. Existing TG libraries are often tailored to specific architectures, hindering support for diverse models in this rapidly evolving field. Additionally, the divide between continuous- and discrete-time dynamic graph methods (CTDG and DTDG) limits direct comparisons and idea transfer. To address these gaps, we introduce Temporal Graph Modelling (TGM), a research-oriented library for ML on temporal graphs, the first to unify CTDG and DTDG approaches. TGM offers first-class support for dynamic node features, time-granularity conversions, and native handling of link-, node-, and graph-level tasks. Empirically, TGM achieves an average 7.8x speedup across multiple models, datasets, and tasks compared to the widely used DyGLib, and an average 175x speedup on graph discretization relative to available implementations. Beyond efficiency, we show in our experiments how TGM unlocks entirely new research possibilities by enabling dynamic graph property prediction and time-driven training paradigms, opening the door to questions previously impractical to study. TGM is available at https://github.com/tgm-team/tgm

cs.LG↗

arXiv2025

Scalable and Cost-Efficient de Novo Template-Based Molecular Generation

Template-based molecular generation offers a promising avenue for drug design by ensuring generated compounds are synthetically accessible through predefined reaction templates and building blocks. In this work, we tackle three core challenges in template-based GFlowNets: (1) minimizing synthesis cost, (2) scaling to large building block libraries, and (3) effectively utilizing small fragment sets. We propose Recursive Cost Guidance, a backward policy framework that employs auxiliary machine learning models to approximate synthesis cost and viability. This guidance steers generation toward low-cost synthesis pathways, significantly enhancing cost-efficiency, molecular diversity, and quality, especially when paired with an Exploitation Penalty that balances the trade-off between exploration and exploitation. To enhance performance in smaller building block libraries, we develop a Dynamic Library mechanism that reuses intermediate high-reward states to construct full synthesis trees. Our approach establishes state-of-the-art results in template-based molecular generation.

q-bio.BM↗

arXiv2025

Are Large Language Models Good Temporal Graph Learners?

Large Language Models (LLMs) have recently driven significant advancements in Natural Language Processing and various other applications. While a broad range of literature has explored the graph-reasoning capabilities of LLMs, including their use of predictors on graphs, the application of LLMs to dynamic graphs -- real world evolving networks -- remains relatively unexplored. Recent work studies synthetic temporal graphs generated by random graph models, but applying LLMs to real-world temporal graphs remains an open question. To address this gap, we introduce Temporal Graph Talker (TGTalker), a novel temporal graph learning framework designed for LLMs. TGTalker utilizes the recency bias in temporal graphs to extract relevant structural information, converted to natural language for LLMs, while leveraging temporal neighbors as additional information for prediction. TGTalker demonstrates competitive link prediction capabilities compared to existing Temporal Graph Neural Network (TGNN) models. Across five real-world networks, TGTalker performs competitively with state-of-the-art temporal graph methods while consistently outperforming popular models such as TGN and HTGN. Furthermore, TGTalker generates textual explanations for each prediction, thus opening up exciting new directions in explainability and interpretability for temporal link prediction. The code is publicly available at https://github.com/shenyangHuang/TGTalker.

cs.CL↗

arXiv2024

Best of Both Worlds: Advantages of Hybrid Graph Sequence Models

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

cs.LG↗

arXiv2024

TGB 2.0: A Benchmark for Learning on Temporal Knowledge Graphs and Heterogeneous Graphs

Multi-relational temporal graphs are powerful tools for modeling real-world data, capturing the evolving and interconnected nature of entities over time. Recently, many novel models are proposed for ML on such graphs intensifying the need for robust evaluation and standardized benchmark datasets. However, the availability of such resources remains scarce and evaluation faces added complexity due to reproducibility issues in experimental protocols. To address these challenges, we introduce Temporal Graph Benchmark 2.0 (TGB 2.0), a novel benchmarking framework tailored for evaluating methods for predicting future links on Temporal Knowledge Graphs and Temporal Heterogeneous Graphs with a focus on large-scale datasets, extending the Temporal Graph Benchmark. TGB 2.0 facilitates comprehensive evaluations by presenting eight novel datasets spanning five domains with up to 53 million edges. TGB 2.0 datasets are significantly larger than existing datasets in terms of number of nodes, edges, or timestamps. In addition, TGB 2.0 provides a reproducible and realistic evaluation pipeline for multi-relational temporal graphs. Through extensive experimentation, we observe that 1) leveraging edge-type information is crucial to obtain high performance, 2) simple heuristic baselines are often competitive with more complex methods, 3) most methods fail to run on our largest datasets, highlighting the need for research on more scalable methods.

cs.LG↗

arXiv2024

$\texttt{MiniMol}$: A Parameter-Efficient Foundation Model for Molecular Learning

In biological tasks, data is rarely plentiful as it is generated from hard-to-gather measurements. Therefore, pre-training foundation models on large quantities of available data and then transfer to low-data downstream tasks is a promising direction. However, how to design effective foundation models for molecular learning remains an open question, with existing approaches typically focusing on models with large parameter capacities. In this work, we propose $\texttt{MiniMol}$, a foundational model for molecular learning with 10 million parameters. $\texttt{MiniMol}$ is pre-trained on a mix of roughly 3300 sparsely defined graph- and node-level tasks of both quantum and biological nature. The pre-training dataset includes approximately 6 million molecules and 500 million labels. To demonstrate the generalizability of $\texttt{MiniMol}$ across tasks, we evaluate it on downstream tasks from the Therapeutic Data Commons (TDC) ADMET group showing significant improvements over the prior state-of-the-art foundation model across 17 tasks. $\texttt{MiniMol}$ will be a public and open-sourced model for future research.

cs.LG↗

arXiv2024

Reducing the Cost of Quantum Chemical Data By Backpropagating Through Density Functional Theory

Density Functional Theory (DFT) accurately predicts the quantum chemical properties of molecules, but scales as $O(N_{\text{electrons}}^3)$. Sch\"utt et al. (2019) successfully approximate DFT 1000x faster with Neural Networks (NN). Arguably, the biggest problem one faces when scaling to larger molecules is the cost of DFT labels. For example, it took years to create the PCQ dataset (Nakata & Shimazaki, 2017) on which subsequent NNs are trained within a week. DFT labels molecules by minimizing energy $E(\cdot )$ as a "loss function." We bypass dataset creation by directly training NNs with $E(\cdot )$ as a loss function. For comparison, Sch\"utt et al. (2019) spent 626 hours creating a dataset on which they trained their NN for 160h, for a total of 786h; our method achieves comparable performance within 31h.

cs.LG↗

arXiv2023

Resource-constrained knowledge diffusion processes inspired by human peer learning

We consider a setting where a population of artificial learners is given, and the objective is to optimize aggregate measures of performance, under constraints on training resources. The problem is motivated by the study of peer learning in human educational systems. In this context, we study natural knowledge diffusion processes in networks of interacting artificial learners. By `natural', we mean processes that reflect human peer learning where the students' internal state and learning process is mostly opaque, and the main degree of freedom lies in the formation of peer learning groups by a coordinator who can potentially evaluate the learners before assigning them to peer groups. Among else, we empirically show that such processes indeed make effective use of the training resources, and enable the design of modular neural models that have the capacity to generalize without being prone to overfitting noisy labels.

cs.LG↗

arXiv2023

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

cs.LG↗

arXiv2022

Generalized Laplacian Positional Encoding for Graph Representation Learning

Graph neural networks (GNNs) are the primary tool for processing graph-structured data. Unfortunately, the most commonly used GNNs, called Message Passing Neural Networks (MPNNs) suffer from several fundamental limitations. To overcome these limitations, recent works have adapted the idea of positional encodings to graph data. This paper draws inspiration from the recent success of Laplacian-based positional encoding and defines a novel family of positional encoding schemes for graphs. We accomplish this by generalizing the optimization problem that defines the Laplace embedding to more general dissimilarity functions rather than the 2-norm used in the original formulation. This family of positional encodings is then instantiated by considering p-norms. We discuss a method for calculating these positional encoding schemes, implement it in PyTorch and demonstrate how the resulting positional encoding captures different properties of the graph. Furthermore, we demonstrate that this novel family of positional encodings can improve the expressive power of MPNNs. Lastly, we present preliminary experimental results.

cs.LG↗